Genomics-guided approaches to enzyme discovery in disparate Galdieria species

Galdieria是一种红色藻类，在高度酸性和高温条件下表现出巨大的繁衍能力。它显示了广泛的代谢能力，几乎可以在任何碳源上实现旺盛的生长。加迪亚是新陈代谢的主力。了解Galdieria在不同生长条件下的代谢能力可以评估该生物体的生物燃料、抗氧化剂和材料化学潜力。这项应用是为了发现Galdieria酶在未经处理的木质纤维生物质的生物转化中发挥作用，用于液体燃料的生物能源生产。我们希望使用参考基因组来促进转录组学和蛋白质组学来指导酶的发现。在第一阶段，将对通过系统学鉴定发现的不同Galdieria不同分支的大量不同碳水化合物介质组成的诱导转录物进行基因组学检查。生长介质来源包括可溶性碳水化合物和糖醇混合物以及复杂的不溶残留物，如淀粉和麦草。这将产生数据集来揭示Galdieria中新的木质纤维降解酶。这些RNA将被量化，并将与对照进行比较，以找到那些诱导表达上调的基因，这些基因可以被注释为分解代谢酶。注释酶的列表将通过对比试验进行关联，以将转录组与Galdieria基因组进行比较。在第二阶段，将对Galdieria的酶进行蛋白质组学调查。在复杂的废物上生长的Galdieria菌株的部分将被用于质谱学。对合成多肽的鉴定指导了进一步的注释。这些鉴定出的蛋白质将与诱导的RNA进行比较。总而言之，从基因组到转录组再到排泄的蛋白质组的全面蛋白质清单将统一起来，这将为这些酸性和热稳定蛋白质的重组形式的酶学服务。

Galdieria is a red alga that displays enormous capacity to thrive at highly acidic conditions and elevated temperatures. Itdisplays broad metabolic repertoires allowing vigorous growth on virtually any carbon source. Galdieria is a metabolicworkhorse. Understanding the metabolic capacity of Galdieria under differing growth conditions assesses the biofuel,antioxidant and materials-chemistry potential for this organism. This application is to discover Galdieria enzymes thatwork in the bioconversion of untreated lignocellulosic biomass for bioenergy production of liquid fuels. We wish to usethe reference genome to facilitate transcriptomics and proteomics to guide enzyme discovery.In phase 1 a genomics examination will be performed of induced transcripts as a result of numerous, differingcarbohydrate-media compositions of differing clades of Galdieria discovered through phylogenomic identification. Thesegrowth-media sources include soluble carbohydrate and sugar-alcohol mixtures and complex insoluble residues suchas starch and wheat straw. This generates data sets to reveal novel lignocellulosic degradation enzymes in Galdieria.The RNAs would be quantified and comparisons to the control would be performed to find those genes induced inexpression that can be annotated as catabolic enzymes. The list of annotated enzymes would be correlated fromcompared tests to associate the transcriptomics compared to the Galdieria genome. Together a list of genes would becomplied for future exploration of encoded activity.In phase 2 a proteomics survey would be performed of enzymes from Galdieria. Fractions of Galdieria strains grown oncomplex wastes would be applied to mass spectroscopy. The identification of resultant peptides guides furtherannotation. These proteins identified will be compared to the induced RNAs. In total a comprehensive list of proteins willbe unified from the genome to the transcriptome to the excreted proteome and this serves enzymology of recombinantforms of such acid and heat stable proteins.